The Stanford Undergraduate and the Mentor

On a weekend in March almost three years ago, Ellie Clougherty flew from London to Rome with Joe Lonsdale. She was a 21-year-old junior at Stanford University, and it was her first trip to Italy. Lonsdale, then 29, was a Silicon Valley entrepreneur, and he booked a room for them for two nights in a luxury hotel — a converted Renaissance mansion in the shadow of the Pantheon — and arranged a special excursion, with a friend of his who is an architect, to an archaeological site amid the ruins of the Golden House on Palatine Hill, overlooking the Colosseum. Under a light gray sky, they stood on plexiglass bridges and looked down at the uncovered remains of what is thought to be a fabled rotating dining room that the Emperor Nero built for extravagant banquets. Lonsdale is a Roman-history buff, and he told Clougherty about the emperors, praising their civilization and engineering feats.

The couple also went with Lonsdale’s friend to the Vatican. Clougherty, who is Catholic, was wearing a short dress and a light cardigan. For modesty’s sake, she draped Lonsdale’s sport coat over her shoulders and tied her sweater around her waist. As she walked with reverence in St. Peter’s Basilica, she recalls, she touched the foot of a bronze statue of St. Peter and, as many believers do, made a wish. “I asked if God would help me with whatever was happening between me and Joe,” she said, in one of many conversations we had over the past seven months. “It was like, ‘I don’t quite understand what this is, but please help.’ ”

Clougherty and Lonsdale had been dating over the previous couple of weeks, while he was her assigned mentor for an undergraduate course at Stanford called Technology Entrepreneurship, Engineering 145. The limited-enrollment class offered a combination of academics, business skills and access to Silicon Valley that has made Stanford the most-sought-after university in the country, with the most competitive undergraduate admissions and among the highest donations. More than any other school, Stanford is the gateway to the tech world, and computer science is the most popular major. Each year, new young multimillionaires are minted, some just months after graduation.

Lonsdale, who also went to Stanford, made much of his fortune by helping to start Palantir Technologies, a major data-mining company. He was among the “top entrepreneurs and venture capitalists,” according to the course description, many of them alumni, who came to campus as mentors for E145. “Students will learn how to tell the difference between a good idea in the dorm and a great scalable business opportunity,” the E145 handbook for mentors says. “Guide them and challenge them.” Stanford students are well aware of how valuable these contacts are. Around the time Clougherty took E145, another student’s project, a virtual-payment app, attracted an investment from a Google board member who was a guest speaker in the course. It became the start-up Clinkle, with initial financing of $25 million.

After sightseeing in Rome, Lonsdale and Clougherty were together in the hotel room they were sharing when she started dressing for evening Mass. Lonsdale came up behind her and kissed her, touching her neck and hair and telling her she was beautiful. She had told him she was a virgin. Both agree they had sex. But what actually went on between them that night, and throughout their yearlong relationship, would become highly contested. After the relationship ended, Clougherty accused Lonsdale of sexual assault. Stanford investigated whether he broke the university’s rule against “consensual sexual and romantic relationships” between students and their mentors and, later, whether he raped her. The findings from the investigations have sparked a war of allegations and interpretations, culminating last month with dueling lawsuits, filled with damaging accusations. This case, which has been picked up by the media, does not fit neatly into the narratives that have fueled an ongoing national conversation about sexual assault of students on campus. But it exposes the risks of Stanford’s open door to Silicon Valley and the pressure that universities are under to do more for students who say they’ve been raped. It also reveals the complexity of trying to determine the truth in a high-stakes case like this one.

Growing up in the suburbs of Fairfax County, Virginia, Clougherty thought at one point about becoming a nun. She set that idea aside by age 15 as she became interested in neuroscience. By then she was also a professional model. Clougherty is 5-foot-10, lithe and blond, with an open, “almost luminous” presence, as one of her professors put it. Traveling to catalog shoots for companies like Target and Kohl’s, she missed a lot of school. Her closest relationship was with her mother, Anne, a former systems engineer who sold a software company in 2000 that she started with her brothers and then continued to work for part time. She accompanied her daughter when she modeled, while her husband, an anesthesiologist, stayed home with her three younger brothers.

Anne took care to protect her daughter from unwanted attention from men. When Clougherty was 10, her family says, a man accosted her in a restaurant on her way to the bathroom. As a teenager trying out for modeling jobs, she would put on heels and makeup for casting calls. “I looked so much older than I was,” Clougherty said. “There were always just a lot of men, complete strangers, on the subways and in the streets, blocking me off or following me, touching my breasts, grabbing my arm. I’d have to walk through them.”

Arriving at Stanford in 2009, Clougherty reveled in the spacious bounty of the California campus. “Everything was literally amazing,” she said. Like a lot of her peers, she felt drawn to the powerful industry next door but also anxious about how to find a footing. To network, she frequently went to tech events and mixers, collecting business cards from alumni and others who came to mingle with students.

Men hold 60 to 70 percent of the jobs at major tech firms, and almost half of tech companies have no female executives at all. Even more than in older, button-down industries, sexual-power dynamics can affect who advances. Many women told me that because they are in the minority, they often find themselves in the role of supplicant when trying to get a job or funding and that men often see professional interactions as sexual opportunities. One Stanford student told me about a male friend who dropped out to start a company and expressed interest in her programming skills. She felt pleased and then realized he saw her only as a datable girl. Another woman, who founded a start-up, described a similar situation. A male executive introduced her to another more powerful man, at a mostly male conference, which she appreciated until it slowly became clear that “he was trying to become friends with this very successful entrepreneur by delivering me,” she said.

At the tech events that Clougherty went to, she was one of few women, and when men pursued her, she often felt overwhelmed and intimidated. She told her mother about it and could feel Anne’s concern radiating through their daily texts and phone calls. In the winter of her sophomore year, Clougherty developed an eating disorder. “I wanted to be invisible,” she told me. Alarmed, Anne flew from Virginia and spent two weeks on campus trying to get her daughter back on track.

Image

At Stanford, a complex relationship between a student and a Silicon Valley entrepreneur is under scrutiny.CreditIan Allen for The New York Times

But Clougherty was struggling, and she withdrew from her classes and went home for therapy for her eating disorder, including eight days of inpatient treatment. That spring, she took a trip with her mother to New York, where a photographer they had met through her modeling work introduced her to a friend of his from the tech world: Joe Lonsdale.

Lonsdale has blue eyes and a wide smile. He grew up in middle-class Fremont, Calif., surrounded by his father’s large extended Irish-Catholic family. He was raised Jewish by his mother, who died when he was 25. At Lonsdale’s elementary school, his father started a chess team that became one of the most successful in California, and the son memorized hundreds of the sequences of moves played by 19th-century masters on his way to becoming a Scholastic chess champion. He learned to code in junior high school and spent most of his time in front of the computer or hanging out in dens and basements with other boys.

As a Stanford student, he edited the conservative Stanford Review, where he encountered Peter Thiel, its co-founder. Lonsdale advanced in a group of male libertarians who saw the valley as a meritocracy built on pure talent. When Lonsdale graduated in 2004 with a degree in computer science, he went to work for Thiel, who created PayPal. Helping the company fight hackers, Lonsdale learned about weaknesses in the government’s surveillance systems and saw a business opportunity. “In the valley, people thought we were crazy, because you’re not supposed to build a business based on deals with the government,” he told me. “We had this very divergent big mission.”

With early funding from the C.I.A., Lonsdale helped Thiel and others start Palantir. Named for the “seeing stones” in “The Lord of the Rings,” the company developed powerful data-mining software for surveillance and won contracts with hundreds of law-enforcement agencies, including the National Security Agency and the Defense Department. In 2009, Lonsdale went on to other ventures but retained a stake in Palantir, whose value would climb to more than $9 billion. In 2011, with a small group of partners, some of whom had close ties to Asia, Lonsdale started the venture-capital fund Formation 8, named for a lucky number in China. Along with starting and financing companies, he has continued to embrace libertarian causes and recently joined the finance team for Senator Rand Paul’s possible Republican presidential campaign. And he sometimes can’t resist showing off his newfound wealth: For a viewing party of HBO’s “Game of Thrones” last year, Lonsdale bought a $30,000 replica of the show’s iron throne, posing on it like the show’s line of blustering and sadistic kings.

After meeting in New York, Clougherty and Lonsdale struck up an intermittent, bantering email correspondence. Lonsdale mentioned that he had a serious girlfriend. But when Clougherty went back to Stanford in the fall of 2011 for her junior year, he asked her to meet him at a Palo Alto bar for a drink. “I’d love to get together and learn more about your ambitions,” he wrote.

The following January, Clougherty started E145, which was part of her self-designed major in management science and neuroengineering. She imagined some day starting a company that would find a socially responsible application of neurological research. The E145 professor matched Clougherty’s team of four students with two mentors. Then Clougherty got an email from Lonsdale. “Ellie — is this the class you’re in/do you require mentorship? haha,” he wrote, forwarding a general query the teacher had sent him about mentoring for the course, which Lonsdale had done previously. Later that day, Lonsdale was switched onto Clougherty’s team. In the first weeks of the course, Clougherty and Lonsdale met with other students on the team, and also met alone.

Late at night on Feb. 7, 2012, Clougherty texted her mother:

“Joe really really really seriously likes me.”

“Yikes,” Anne wrote back. “How does this keep happening :)”

“I’ve stopped questioning it,” Clougherty answered. “There’s nothing I can do at this point; thought I could control it once but no, nope, can’t, it’s now officially inevitable.” Emailing a few days later, Clougherty and Lonsdale discovered they were each going to Europe for spring break, and Lonsdale invited her to Rome. “You are darling,” he wrote when she asked a question about how personalities can interfere with work in the tech field.

Clougherty’s emails to Lonsdale welcomed his attention. “HAPPY VALENTINES DAY JOE LONSDALE!” she wrote. “I hope to spend more time with you in the near future! Your kindness, integrity, desire to make the world a better place and willingness/confidence to make it happen is severely unique and an incredible thing to witness.” Lonsdale was smitten. He told me that toward the end of his two-year relationship with his previous girlfriend, who was closer to his age, he would feel like “I was in trouble all the time” for working obsessively. But Clougherty was “this amazing young woman, so energetic and positive. She made me feel like everything I was doing was special.”

Anne was impressed by Lonsdale’s professional accomplishments, but as we drove through Virginia in October, she said she initially wondered what he saw in her college-age daughter. Anne is a tall, attractive and forceful presence, and she said that at the end of February, she flew to California for parents’ weekend at Stanford, and Clougherty arranged a dinner with Lonsdale. At first, Anne found him awkward. He had a hard time making eye contact, and she noticed his facial tic. (He cuffs his chin with his fist and grimaces.) But her doubts melted, she says, when he promised to guard her daughter from the valley’s wolfish atmosphere. Lonsdale says that the subject did not come up then, but that later he tried to shield Clougherty from other men. “She said guys were coming after her, and it got me angry,” he told me. “She’s very beautiful, and you want to protect her.”

A week later, Lonsdale gave Clougherty a dozen roses and took her on a picnic with caviar, crème fraîche and sparkling wine in a basket packed by his assistant. Instead of studying at the campus library, Clougherty sat by his fireplace to write her business plan for class. On Lonsdale’s bed, she found a gift of silk pajamas, which she reported to her mother with an “:O,” for open-mouthed. A couple of weeks later, he gave her a book about Julius Caesar, with the inscription “To Ellie — who helps me see the world with a new sense of wonder. Let’s explore and conquer together.” Because Clougherty already had plane tickets for her trip to Europe, her mother emailed with Lonsdale’s assistant about rearranging her daughter’s itinerary. Lonsdale and Clougherty planned to meet in London, and he bought her a ticket for his flight to Rome.

When Clougherty got back to campus in April, she had a newly glamorous life. Lonsdale sent cars to pick her up at her dorm so she could meet him in San Francisco. They saw each other regularly, carving out time between her classes and his fund-raising trips for Formation 8. One friend of Clougherty’s told me that she occasionally went out with the couple to extravagant events: “It was a cool life to be living — I thought she was experiencing a lot.” But Jane, another friend of Clougherty’s, whom she had known since freshman year, was more skeptical. She said she thought that Lonsdale was too old for Clougherty and told her so. After the Rome trip, it took Clougherty a few weeks to tell Jane, who asked me to use her nickname, that she had lost her virginity. “Before that, she’d said that as a Catholic, she wanted to wait for marriage, so she didn’t want to admit it,” Jane said. “But when she did tell me, she made being with Joe sound romantic.”

Late in April, Lonsdale and Clougherty flew to New York, where they met her mother. He got the three of them on the list for a posh event on the top of the Standard Hotel for the Tribeca Film Festival. Anne began to ask Lonsdale for his advice about business ventures, including one to rebrand Haitian products like coffee and chocolate. “If you could give me an introduction,” she wrote in an email after seeing him in New York, “that would be great.”

Clougherty and Lonsdale started talking about a summer project she could do for Formation 8. They settled on a survey of “disruptive” technology, and Clougherty invited a friend from high school, Rachel, to come to California and work on it with her. Anne found them an apartment in Palo Alto. Lonsdale paid the rent. “It was a very weird summer,” Rachel told me over Skype. Lonsdale flew her and Clougherty to New York in July for a swank networking event and put them up at the St. Regis. But the survey they were supposed to complete went unfunded and unfinished. Spending evenings with Lonsdale and Clougherty, Rachel felt like a third wheel. She also found Lonsdale condescending. When Lonsdale hosted dinners at his house with other executives, Rachel said, she and Clougherty were sometimes the only women, and Rachel felt they were belittled. Sometimes Clougherty would sit on his lap. “It was like she was the pretty wallpaper,” Rachel said. He talked about marrying Clougherty and made jokes like, “ ‘I have no power with you — I’m a powerful man but I’m at your mercy,’ ” Rachel said. Clougherty told me that she wanted to believe she and Lonsdale could eventually be equals, using their joint influence for good. “I thought it would be so nice to have the chance to have an impact,” she said. “There are respectable women married to respectable guys in the valley. I wanted to think, I could be happy like that, too.”

In emails Clougherty wrote at the time, she told Lonsdale that she found him attractive. “Kiss kiss kiss, you are super handsome,” she wrote in June, and later, “You are a sexy man” and “It was so nice sleeping with you.” But around the same time, she also told Rachel that she never wanted to have sex with Lonsdale, beginning in Rome. “She said, ‘I don’t want to be having sex, but he’s not listening to me,’ ” Rachel said.

Rachel said she thought Lonsdale was manipulating Clougherty into spending the night at his house. “I could see on her face that she didn’t want to go, and then he’d start his trick. ‘You don’t want to spend time with me?’ ” Rachel talked about her concerns with Anne. Together they counseled Clougherty to explain to Lonsdale that she did not want to be spending nights with him. She said she did, but the nights together continued. “They had sex again, and she was upset about it, clearly,” Rachel said. “I reacted strongly. I said, ‘This is your decision.’ Her mom was there too. Then I realized Ellie felt a little upset. She felt we were judging her.”

Around the same time, Anne was emailing with Lonsdale about his plans to buy a new house. During that summer, she came out to look at real estate with the couple and attended the wedding of Lonsdale’s father. Lonsdale’s younger brother and other relatives complained that Anne was inserting herself into every corner of his life, and worried that she and Clougherty were after his wealth. But he brushed them off. “They thought I was a naïve guy screwing up, but I was in love,” he said.

In August, Lonsdale took Clougherty on a 10-day trip to raise money for Formation 8 in Hong Kong, Beijing and Seoul. Clougherty had no official role, but she was thrilled to be included in high-level meetings, with industry leaders like the chief executive of the Internet giant Baidu, and prided herself on helping Lonsdale. “I was on high alert to absorb everything I could, so I could be socially aware for him,” she said. “Like if he wasn’t fully listening to someone, I would say a few lines to cover.” At the end of the trip, she expressed gratitude, writing to Lonsdale, “I love how much you trust me to bring me to all your meetings bc I literally couldn’t imagine a more awesome thing I’d rather do!”

But the trip also had difficult patches. In an email Lonsdale wrote to Clougherty after they returned, he acknowledged that she complained about not eating regularly and that they argued about religion. After they got home, she found old copies of Playboy magazine in his bureau drawer and became furious. Lonsdale told her she was overreacting. “I am really scared by how you are super positive about me one day — too much so — and then super negative the next,” he emailed. “This binary swinging between things is hurtful, and it’s also very immature.” She apologized in a long letter that described her struggle to recover from her eating disorder the previous year, including the inpatient treatment, which she had found terrifying. “Sometimes I think it would have been so much better had you met me a year from now, when I’m fully healed,” she wrote. Lonsdale thanked her for being open. “I think you will be all healed soon, and I hope I can help,” he wrote.

At the end of September, Lonsdale rented out the Hearst Castle, on the California coast, for a lavish 30th-birthday party with hundreds of guests. He was also celebrating the third anniversary of Addepar, a data-based platform for wealth management that he co-founded. The company’s logo, lit from behind, loomed above an outdoor pool at the castle. Clougherty’s parents flew out for the occasion, taking to the dance floor while their daughter circulated as hostess, wearing an embroidered cream-colored gown by Sue Wong that she and her mother shopped for. “It was like being a princess at a ball,” she told me. “It seemed magical on the surface.” At the end of the evening, Lonsdale broke the castle rules by jumping into one of the pools.

But over the autumn and winter, their relationship frayed. Lonsdale hit a crucial period of fund-raising for Formation 8, and Clougherty expressed resentment when he would ask her to come over late at night. He responded impatiently. “I don’t know what analogy makes sense to you, and Odysseus is probably not the right one,” he wrote in the fall. “But I am on a really big, difficult, critical mission the next several weeks.” It would be hard for the relationship to work, he warned, “if my darling is actually just sort of annoyed at me and isn’t in a position where of course she is eager to see me anytime I can.”

In December 2012, Lonsdale wrote Clougherty a long email. “We are dealing with serious relationship dysfunction,” he began, and laid out a list of examples in bullet points. The first read: “Sometimes I feel it’s very clear you are eager to engage sexually, but other times you will talk about me taking advantage of you and forcing myself on you as if there is this dirty old man/young innocent student dynamic, and I should feel badly about it. We will do something and then just a bit later you’ll talk as if ‘how can I stop you from making me do that?’ and yet earlier I honestly thought you wanted to.”

Image

Joe Lonsdale and Ellie Clougherty in Rome, March 2012.CreditPhotograph from Joe Lonsdale

Lonsdale spent Christmas with Clougherty at her family’s home. They fought about a number of things, including the fact that he didn’t bring her a Christmas present. When he got home, Lonsdale broke up with her over email. When she returned to Stanford in the beginning of January, they started seeing each other again for what they called a trial period. Jane told Clougherty that she thought it was a bad idea for them to get back together. She says Clougherty told her that Lonsdale wanted to have sex “all the time” and that during it, he would put his hand on her throat. She didn’t think her friend was ready for the sexual relationship that Clougherty said Lonsdale wanted.

On Jan. 7, she texted Anne: “I’m scared for Ellie. I don’t want her with Joe at all. In fact, I worry about her safety. The guy is a jackass. What’s going on there? I feel like I may be the only one at school who can look out for her.”

“I think you r the only one who looks out for her,” Anne said.

“But what is she thinking?” Jane replied. “From what I’ve heard it sounds horrific and the guy is a psycho. I feel like I’ve failed her because she doesn’t realize she doesn’t have to put up with someone like that. There are so many other unbroken people out there. Anne, I hate to say this but this guy definitely seems like the type who would abuse her.”

“Hmm,” Anne responded. “I don’t think he is that aggressive. More like a little clueless.”

But in a mid-February phone call, Clougherty told her mother that she was having a hard time making it to class, was not eating and was spending hours in her dorm room alone. Anne was worried. “I was saying, ‘Why can’t you just not be with him, why can’t you go to class, why can’t you go to the cafeteria, why can’t you be in control of your life?’ ” Anne said. “Over the phone, there were just these long silences. I thought, Something is dramatically wrong with her.”

Clougherty’s fragility reminded Anne of the state her daughter was in when she had to leave school more than a year earlier. She decided to go to California again. On the flight, she read a book suggested by a friend who had been in an abusive relationship called “Why Does He Do That?: Inside the Minds of Angry and Controlling Men,” by a domestic-violence counselor, Lundy Bancroft. The book riveted Anne. She saw Lonsdale in the descriptions of an abuser and she saw Clougherty in the role of a victim in denial. Anne got to Stanford bent on an urgent rescue. “I was bringing my daughter home no matter what,” she said.

Anne took her daughter to a hotel and gave her Bancroft’s book. Clougherty stayed up late reading and writing, going back and forth between the book and her computer. The next morning, sitting up in bed, she typed furiously on her laptop: “If I said no, he would slowly convince me/make it look like he was going to die if I didn’t climb on top of him. He would freak out when I mentioned I wanted to slow things down, even if it meant having sex only once each time I would see him. One time I cried hysterically because it freaked me out and he wouldn’t listen to me but he would then immediately start crying way harder than me saying he felt like a creepy old man and didn’t want to feel that way. I felt compelled to comfort him even though I was the one who felt violated.”

Clougherty decided she wanted to “escape.” She met Lonsdale in a Palo Alto park in late February, and they broke up while Anne and Jane waited for her in a nearby wine bar. When Anne went home a few days later, Jane tried to help Clougherty by deleting Lonsdale from her Facebook account and taking her out bowling and for ice cream.

“There has to be zero contact,” Jane texted Anne.

On March 1, Clougherty went to Stanford’s counseling center. She said that Lonsdale had forced her to have sex when she didn’t want to and also talked about the man who accosted her in the restaurant bathroom when she was 10. The university psychologist noted in a report that she “seems to have symptoms of post-traumatic stress disorder from current and past trauma.” Clougherty went home to Virginia and spent days crying and rocking in a corner of her family’s living room. Clougherty embarked on therapy twice a week with Keith Saylor, a clinical psychologist who treated her eating disorder. He used prolonged-exposure therapy, a treatment developed for combat-related disorders, in which a therapist prompts a patient to describe deeply traumatic events. Later, patients listen to tapes of their sessions at home every day in an attempt to drain the memories of their power.

With Clougherty’s permission, I listened to tapes of their 90-minute sessions. As he typically does when conducting prolonged-exposure therapy, Saylor reflected back Clougherty’s account, saying that she had experienced “multiple traumas over a prolonged period of time that did repeated damage.” In one session, he told Clougherty, repeating her words, that Lonsdale “held you captive,” continuing, “You were essentially brainwashed over a year.”

On the tapes, Clougherty swallows sobs and speaks in a thin, small voice. She described particular sexual acts that she didn’t want to take part in and how Lonsdale cajoled, begged and insisted until she gave in. She also said that during sex he slapped and shoved her and put his hands around her neck. “It was rape in a sadomasochist way nine times a day,” she said. In a later session, Saylor again mirrored what she told him: “You didn’t have personal agency, you didn’t have personal choice, all of those things had been robbed from you.”

Initially, Clougherty told Saylor, as she had said to her friends, that she had sex for the first time with Lonsdale in Rome. Weeks into therapy, Clougherty said that early in the mentorship for E145, Lonsdale picked her up around 10 p.m. near campus for what she thought would be a quick dinner nearby so they could talk about the class project. Without asking, she said, he took the highway south to his house in the Los Altos hills. When they went inside for dinner, Clougherty said, he surprised her by yanking her into a bedroom located off the kitchen and throwing her down on a king-size bed covered with a fur spread. He raped her, she said. Lonsdale denies that he drove her to his house without inviting her first and says he never raped her.

Image

The Center for Engineering Management, where Ellie Clougherty had Joe Lonsdale as a mentor.CreditIan Allen for The New York Times

Before she went into therapy, Clougherty told me, she didn’t want to admit even to herself that she had been raped. She wanted to believe that the relationship was loving, and she also felt she had a lot to lose. “It was like I could call him a rapist, and I could get judged and get in big trouble and not know how to handle it or I could say, ‘He’s great, look at these emails, I want to date that person,’ ” she said. “Trauma therapy was the first time I felt allowed to talk about how I felt.”

In the course of the therapy, Clougherty came to reject the term “relationship,” or even “abusive relationship,” to characterize her year with Lonsdale. She now calls it a “psychological kidnapping,” a term she came up with after watching a video about domestic abuse on the Internet, and she says she was raped every time she and Lonsdale had sex. Saylor, who agreed to speak with me at Clougherty’s request, said, “People in these kinds of dramatic circumstances sometimes don’t tell anyone.” He also said that prolonged-exposure therapy doesn’t “encourage perspective-taking” and that Lonsdale might have an entirely different view of the relationship. “My role is not to question her veracity but to help her get well.”

Clougherty finished her coursework for Stanford online when she was at home. During that time she decided she wanted Stanford to intervene. In May 2013, she and her parents went back to campus to ask the university to investigate Lonsdale’s conduct. Her friend Jane saw this as a setback for Clougherty: “I said, ‘Oh, no, you should move on.’ ”

Meanwhile on campuses throughout the country, a movement was taking shape. A growing number of students were coming forward to criticize their universities for the handling of sexual-assault cases. They had support from the government. In 2011, the Office of Civil Rights in the Department of Education sent a letter to every college and university in the country that receives federal funding, as almost all do, clarifying that under Title IX, the federal law passed in 1972 to prevent sex discrimination in education, colleges and universities had an obligation to prevent and respond to sexual violence and harassment. “Once a school knows or reasonably should know of possible sexual violence, it must take immediate and appropriate action to investigate or otherwise determine what occurred,” the letter from the Office of Civil Rights warned.

The government also instructed schools to adopt a new standard for determining the outcome of a sexual-harassment or violence case. At the time, many schools used the standard of “clear and convincing” evidence, meaning that the adjudicators (usually a panel of administrators or faculty) believed that it was substantially more likely than not, or roughly 75 percent likely, that the accused had committed the offense. The letter from the civil rights office demanded that schools switch to a lower standard of proof, a “preponderance” of evidence, meaning that it was more likely than not — above 50.01 percent — that the offense was committed. The office noted that preponderance is the standard that courts use to decide civil suits for sexual harassment. A few schools, including Princeton and Harvard, initially refused the new standard and then found themselves under investigation for suspected Title IX violations.

Stanford quickly followed the mandate by adopting the preponderance standard. The university also adopted a policy requiring full investigations when students reported sexual harassment and assault. In May 2013, Clougherty submitted to Stanford a written account of her sexual-assault and harassment allegations, including selected texts and emails. The university appears to have initially investigated only whether Lonsdale broke the rules against consensual relationships between mentors and mentees, which the university treats as “inherently unequal,” like relationships between teachers and students. Stanford said it cannot comment on any sexual-assault case unless a student waives his or her privacy protections under federal law. But Lisa Lapin, a spokeswoman for the university, wrote in an email that in light of these constraints “when unhappy parties tell their version of the stories to the press, it’s no wonder that in virtually every case, the university ends up being portrayed in a highly negative light.”

Marcia Pope, an outside investigator hired by the university, from the law firm Pillsbury, interviewed Lonsdale without a lawyer. He said that he didn’t know about the rule against consensual relationships between mentors and mentees, which is posted on the university’s website but was not included in the mentor handbook for E145. In June, Stanford found that Lonsdale had violated this rule and said he could not mentor undergraduates for 10 years.

Lonsdale was unhappy with the decision, but to Clougherty and her mother, the penalty seemed negligible. They were confused about why Stanford hadn’t looked into her sexual-assault allegations. In November 2013, they attended a conference on gender-based violence at Harvard and heard a talk given by Diane Rosenfeld, a Harvard lecturer and lawyer. “Diane said, ‘You have these rights in Title IX,’ and that’s when it clicked,” Anne said. “I chased her into the bathroom and said: ‘You have to meet my daughter. We need your help.’ ”

Rosenfeld agreed to represent Clougherty in negotiations with Stanford and Lonsdale over her allegations of sexual harassment and assault and gave her a refrigerator magnet with the slogan “You Are Pure Potential.” The next month, Stanford, Clougherty, Lonsdale and their lawyers met for a daylong mediation. Before the meeting Clougherty texted Jane: “Totally joe take down scheme!” (Clougherty says “scheme” wasn’t a good choice of words; she meant she was “taking down a rapist.”) Clougherty settled with the university for an undisclosed amount. A few days later, Clougherty received a settlement proposal from Lonsdale. It contained a blanket nondisclosure provision that Clougherty did not want to sign and the deal fell through. Lonsdale vehemently denies making a settlement offer.

Around the same time, Jane texted Clougherty: “Dude just settle so you can move on. This is going to become your life.”

Shortly after that, Stanford opened a new investigation into Clougherty’s sexual-harassment and assault allegations. Stanford had learned that Lonsdale had dated another student after he and Clougherty broke up. Pope, the outside investigator, started contacting witnesses. She talked to Clougherty’s friend Rachel, who described the troubling sexual dynamic she felt she had seen between Lonsdale and Clougherty over the summer. Pope also spoke to the second Stanford student that Lonsdale dated. Clougherty knew her and was convinced that she had also been abused. But the woman told Pope that her relationship with Lonsdale was consensual and not abusive. When I got in touch with her, she declined to comment.

At the time Stanford was examining Clougherty’s allegation, the school was also addressing fallout from another investigation. Three female students were privately confronting administrators after realizing that they all reported sexual violence, including choking, involving the same male student over three years. According to university documents, the man didn’t deny the choking when Stanford questioned him in 2012 and was allowed to remain on campus. Then last June another case came to the surface. Public protests erupted after Leah Francis, a senior, spoke out when Stanford refused to expel a male student after the university found he had sexually assaulted her. (Since 1997, 25 sexual-harassment and sexual-assault cases have gone through Stanford’s disciplinary process. Ten students have been found culpable; only one was expelled.)

Two weeks later, the university reached a new decision regarding Lonsdale. Stanford now found that he had engaged in sexual misconduct and harassment during his relationship with Clougherty and banned him from campus “for any purpose.” After 10 years, he could apply to return; Stanford “strongly encouraged” him to seek counseling for sexual misconduct and relationship violence.

“When we ask someone to stay away from campus, it’s because we have a concern about that person’s impact on the community and certainly on students,” a senior university counsel, Lauren Schoenthaler, told me. Yet since the ban was imposed last June, Lonsdale has been invited to campus for a private lunch, which he attended with the university’s permission. (Stanford says it declined other requests from Lonsdale to come to campus.) He was also featured on Stanford’s website as a mentor for StartX, a business accelerator that supports companies founded by students. When I asked Schoenthaler in December about Lonsdale’s online university presence, she said StartX would move off Stanford’s website. As of Feb. 6, it was still there.

In the last few months, Stanford and other schools have felt the ground shift beneath them once again. Some critics are now charging that universities are overcompensating for past mistreatment of victims. Even as they’re attacked for giving victims short shrift, schools are also being denounced for inadequately protecting the rights of the accused. In October, 28 members of the Harvard law-school faculty wrote a letter, published in The Boston Globe, deploring the procedures the university adopted to follow the mandate from the Office of Civil Rights for lacking “the most basic elements of fairness and due process” and being “overwhelmingly stacked against the accused.” Around the country, about three dozen men are suing universities over findings or punishments for sexual infractions. In a short span of time, a well-intentioned effort to right a seemingly obvious wrong has fed additional claims of injustice.

Lonsdale says that he believes Stanford’s treatment of him was influenced by student activism and the protests over Leah Francis’s case. “Everyone believes the woman,” he told me in December as we sat at a small conference table in New York for two hours with two lawyers and a public-relations strategist.

Lonsdale seemed nervous, well coached and eager to stress his commitment to gender equality. “It’s important to me to be with a woman I respect,” he said. Since Stanford’s findings against him last June, he has promoted women’s causes, judging a hackathon to fight the sexual exploitation of girls (alongside three women with excellent tech credentials) and writing an article in The Stanford Review with the headline “Economic Conservatives Should Champion Female Technologists.”

Describing his relationship with Clougherty, Lonsdale played down his authority and played up hers. “Ellie is a forceful person,” he said. “If I did anything she thought was wrong, she’d express it.” Later, he stressed the point again, saying, “She is very vocal about what she wants and doesn’t want.” He dismissed his role as her E145 mentor as a “supercasual thing.” He had older friends who also dated undergraduates, he said. “I didn’t think it was any big deal.”

Lonsdale and his lawyers told me that when Pope, the Stanford investigator, asked to interview Lonsdale for a second time in December 2013, he declined and submitted a statement in writing. In Lonsdale’s description of the relationship, he says that he and Clougherty were in love and she never said no to sex or even expressed ambivalence in the moment. I asked about the email he sent shortly before he broke up with her in December 2012, complaining that she sometimes said he was “forcing” himself on her. Lonsdale said the problem wasn’t Clougherty’s lack of consent. It was that she sometimes felt bad after the fact. “There was a lot of stuff around the Catholic guilt,” he said, “about how she didn’t like being addicted to the body.”

Despite all the turns the case had taken, until I asked Lonsdale about it, he said he had never heard Clougherty’s accusation that he raped her that night at his house. It seemed to startle him. “I didn’t rape her,” he said with emotion. “We didn’t have sex until Rome. This is a whole new thing. She is scarred and broken, and she is making stories up.” He looked around at his lawyers and then back at me. “It’s like I’m some sort of crazy monster.”

It’s hard to tell whether Stanford sees Lonsdale as a real threat. In a letter to him and Clougherty in June 2014 after the second investigation, the university stated only that on several occasions Clougherty expressed that she didn’t want “the sexual contact in question.” The university didn’t explain the meaning or limits of this vague phrase. There is no police investigation in this case, no indictment laying out charges and nothing from a judge or jury to specify what Lonsdale was found guilty or not guilty of. Instead of the transparency of open court, Stanford offered opacity.

Stanford’s rules explicitly grant a right of appeal to students, faculty and staff but include conflicting statements about whether other members of the university community may appeal. Lonsdale’s lawyers asked the university to reopen the case once more. In November, after I contacted Lonsdale, his lawyers submitted to Stanford hundreds of pages of his email correspondence with Clougherty and her mother that they hadn’t previously provided. Stanford has not decided whether to consider this evidence, along with an eight-page sworn statement Lonsdale gave the university from an unexpected source: Clougherty’s friend Jane.

In the months after Jane helped Clougherty break up with Lonsdale, she says that she watched with increasing unease as Clougherty’s accusations mounted, from emotional abuse to rape. “In March 2014, she texted me that she considered herself a ‘sex slave’ during her relationship with Joe,” Jane wrote in her statement. “This is far, far beyond anything that she ever said about the relationship when it was happening or for a long time afterward. It also made no sense in light of her clear enthusiasm about the relationship.”

Jane told me by phone that the breaking point in her friendship with Clougherty came when Stanford began the second investigation of Lonsdale. Jane says she thought the investigation was not warranted and told Clougherty that she would not talk to Pope. Clougherty sent her three texts in April 2014: “Hey, all the investigators need to know is that you witnessed my escape from Joe and saw him pounding on the steering wheel.” “Did you really decline to speak with them?” “I don’t understand, I thought you’d support me.” On the night of the break up, Anne and Jane were sitting in the wine bar waiting for Clougherty. They saw Lonsdale drive up with Clougherty. In Anne’s account, she and Jane could see Lonsdale pounding on the steering wheel. Jane jumped up and went outside to knock on the window of the car and make sure Clougherty was O.K.

Jane, though, told me that “the conversation in the car looked completely normal.” She added: “I didn’t go outside. She came in, and I thought, Great! She’s fine, and it’s over.” She gave a short, bitter laugh. “They asked me to lie, and I said no. Ellie yelled at me over the phone.” She gave another short laugh. “She hung up on me after five years of helping her through all her life issues and crises, all the calls from Anne, ‘Will you look after Ellie?’ All of that, only to be put to the side when I won’t do what they want me to do.” She paused. “In retrospect, I understand. I was used.” Clougherty said she never asked Jane to lie: “I didn’t know she was mad at me. We just wanted her to say she was a witness to me breaking up with him.”

Jane, who works in tech, says she got in touch with Lonsdale late last summer. “I thought, He needs to know what I know,” she said. I asked whether she considered that helping Lonsdale might benefit her professionally. “I don’t want to sound like a hero, but I don’t need Joe’s help,” she said. “My job is going great.”

In her sworn statement, Jane wrote, “If I sensed, even remotely, that the relationship was in any way abusive, I would have talked to Ellie’s mom about it.” I asked her about the texts she wrote to Anne two years ago, which conveyed just this sort of distrust of Lonsdale and fear for Clougherty, reading them to her over the phone.

At first, Jane said she didn’t remember writing the messages. She later said she recalled them and the concern she felt then, but said that her fears, which were based on Clougherty’s account, seem exaggerated now that she was older and more experienced herself. She and Clougherty haven’t spoken since their phone call nine months ago.

Clougherty is currently a student at the University of Virginia, enrolled in a master’s program in data science and living with her brother, also a student, in a Charlottesville apartment their mother found them. After Rolling Stone published its story of a lurid fraternity gang rape in November, Clougherty and Anne arranged a meeting with the university president, Teresa Sullivan. On the day before Thanksgiving, they spent a couple of hours sitting in front of a fire at Sullivan’s home, drinking hot chocolate and talking about the effects of trauma. Clougherty gave Sullivan a beaded bracelet she had made and was thrilled when Sullivan mentioned the gift in a major speech on campus the following week, calling Clougherty the survivor of a “brutal assault inflicted on her at another university.”

Rolling Stone soon apologized for its gang-rape story after key facts were discredited. Clougherty and her mother were rattled but undeterred about speaking out. “It’s not an easy decision, but I just see it as a moral obligation,” Clougherty said. “I really want to help other women.” In January, Clougherty filed a civil suit against Lonsdale, accusing him of sexual abuse. She called his behavior “violent and deviant,” saying he employed “psychological manipulation and coercion” including “isolation, sleep deprivation, food deprivation.” She also accused him of “strangling her, slapping her, scratching her, yanking her by the hair so hard that he would lift her torso off the bed and slamming her body against the walls and bed boards.” In addition, she sued Formation 8 for being negligent in its supervision during the summer she was doing the project with Rachel. The lawsuit states that she “wrote him numerous emails and love letters to let him know how much she cared about him in the hope that it would end the abuse.”

In response to Clougherty’s lawsuit, Lonsdale mounted a swift counterattack, calling it “a vengeful, personal attack by a disturbed former girlfriend” in an email to friends and associates. He also said that Stanford’s investigation was “a Kafka-esque nightmare.” He linked to Clougherty’s emails, posting them on a website his team created overnight, highlighting the most affectionate and admiring passages and arguing that she was unstable. Lonsdale also sued Clougherty for defamation. (In the wake of the lawsuits, Formation 8 has been criticized in the press for not disclosing that Lonsdale was banned from Stanford.) He blamed himself only for being naïve.

As this battle is waged in court, Stanford and other universities may improve their handling of future sexual-assault and harassment cases. The policies they have put in place since the government’s 2011 directive will surely turn out to be a draft that they rewrite over time. (Stanford has a task force working on the issue.) Universities are legally obligated to investigate and referee claims like Clougherty’s, and the imbalance of power inherent in these entanglements is of real concern.

At the same time, the role the government has cast universities in is not a natural one. They are not the police. Yet they are asked to grapple with criminal accusations even when the events in question are receding into the past and are deeply difficult to deconstruct. And they are self-interested in a way that courts are not, with a different need: to protect their reputation.

Lonsdale and Clougherty are now moving beyond Stanford. He says he’s relieved to finally confront her accusations in open court. She says going public is liberating. “Now I’m free to live my life, knowing I sent this up into the world and more people can respond to it other than just me.” She has no plans to return to Silicon Valley and says she wants to advocate on behalf of abused women. She’s also looking for a path involving brain research and tech that would include social activism. “My only fear now is that people will judge me, and then if I become a neuroscientist, they won’t believe what I have to say,” she said a few days after filing suit. “It’s a risk, but I have to do this.”

Correction:

An article on Feb. 15 about a sexual-assault allegation misidentified the location in California of the home of Joe Lonsdale, the man who was accused and who has denied the accusation. He lived in the Los Altos hills, not the Los Gatos hills.

Emily Bazelon is a staff writer for the magazine and the Truman Capote Fellow at Yale Law School.